Two thoughts
1) My location (120 Warren) had a sign that said that the prepaid tolls don't cover congestion charge
2) Spending is actually up in a lot of tourist districts because the honking and crazy drivers from NJ/LI are no longer a menace in the city
Traffic Down, Business Up: Governor Hochul Highlights Progress Made Under New York’s Congestion Pricing Program | Governor Kathy Hochul
3) Best advice I can give is to register the rental plate as a rental car under your credit card on the NY/NJ toll website.